Fails to install on Mac OS X 10.11 #135

rustyconover · 2016-01-08T03:16:00Z

> devtools::install_github("igraph/rigraph")
Downloading GitHub repo igraph/rigraph@master
Installing igraph
'/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/bin/R' --no-site-file  \
  --no-environ --no-save --no-restore CMD INSTALL  \
  '/private/var/folders/11/8ydpws752f100kjcy0jzhpdh0000gn/T/Rtmp80DI80/devtoolsaa70783b2c0f/igraph-rigraph-057cc9d'  \
  --library='/usr/local/lib/R/site-library' --install-tests 

* installing *source* package ‘igraph’ ...
....[good lines]...
clang -I/usr/local/Cellar/r/3.2.2_1/R.framework/Resources/include -DNDEBUG -I/usr/local/include  -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include  -I/usr/local/include  -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -g -O2 -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/libxml2 -g -O2 -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"1.1.0\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -g -O2  -c CHOLMOD/Check/cholmod_check.c -o CHOLMOD/Check/cholmod_check.o
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:174:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:174:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:176:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", " , ") ;
        ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:176:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", " , ") ;
        ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:178:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", ")") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:178:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", ")") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:182:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [CHOLMOD/Check/cholmod_check.o] Error 1
ERROR: compilation failed for package ‘graph’

The text was updated successfully, but these errors were encountered:

gaborcsardi · 2016-01-21T15:14:54Z

Looks like you use R from brew. Unfortunately I don't have the time to support that. You can try asking on StackOverflow.

rundel · 2016-02-27T03:53:49Z

I'm seeing the same issue with CRAN installed R when installing the package from source. I do also have homebrew installed and have been using its R distribution - but switching back to a CRAN install I am having the same issue (failure is at the same location for both R distros).

***Good results snipped***
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG  -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include   -DUSING_R -I. -Iinclude -Ics -Iglpk -Iplfit -ICHOLMOD/Include -IAMD/Include -ICOLAMD/Include -ISuiteSparse_config -Wall -mtune=core2 -g -O2 -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/libxml2 -Wall -mtune=core2 -g -O2 -I/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.11.sdk/usr/include/libxml2 -DNDEBUG -DNPARTITION -DNTIMER -DNCAMD -DNPRINT -DPACKAGE_VERSION=\"@VERSION@\" -DINTERNAL_ARPACK -DIGRAPH_THREAD_LOCAL=/**/ -fPIC  -Wall -mtune=core2 -g -O2  -c CHOLMOD/Check/cholmod_check.c -o CHOLMOD/Check/cholmod_check.o
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:170:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [p]) ;
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:174:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:174:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:175:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p  ]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:176:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", " , ") ;
        ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:176:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", " , ") ;
        ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:112:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %23.15e", value) ; \
        ^~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:177:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        PRINTVALUE (Xx [2*p+1]) ;
        ^~~~~~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:116:2: note: expanded from macro 'PRINTVALUE'
        P4 (" %.5g", value) ; \
        ^~~~~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:178:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", ")") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:178:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", ")") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:86:11: note: expanded from macro 'PR'
        (Common->print_function) (format, arg) ; \
         ~~~~~~  ^
CHOLMOD/Check/cholmod_check.c:182:2: error: no member named 'print_function' in 'struct cholmod_common_struct'
        P4 ("%s", "(") ;
        ^~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:93:24: note: expanded from macro 'P4'
#define P4(format,arg) PR(4,format,arg)
                       ^~~~~~~~~~~~~~~~
CHOLMOD/Check/cholmod_check.c:84:31: note: expanded from macro 'PR'
    if (print >= i && Common->print_function != NULL) \
                      ~~~~~~  ^
fatal error: too many errors emitted, stopping now [-ferror-limit=]
20 errors generated.
make: *** [CHOLMOD/Check/cholmod_check.o] Error 1
ERROR: compilation failed for package ‘igraph’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/igraph’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/igraph’

The downloaded source packages are in
    ‘/private/var/folders/k8/4z3ndjqd0nj1xczfp4ktnnzc0000gp/T/RtmpGUZLcI/downloaded_packages’
Warning message:
In install.packages("igraph", type = "source") :
  installation of package ‘igraph’ had non-zero exit status

rundel · 2016-03-01T22:33:39Z

This seems to be related to a couple of issues, see #111 for a fix for the package defined CFLAGS and this for a Homebrew related issue.

A short term fix for me was to uninstall suite-sparse via Homebrew, which removed the CHOLMOD headers that were causing the issue.

ivirshup · 2019-02-12T03:02:29Z

Minor update, brew unlink suite-sparse was sufficient for me to get igraph to install (then ran brew link suite-sparse to quickly re-enable).

pat-s · 2019-11-30T07:13:19Z

Since the above comment has so many upvotes and it also did the trick for me: Is there a chance this can be solved upstream?

(not using R from brew in combination with clang7)

ktmeaton · 2020-07-11T14:30:22Z

Minor update, brew unlink suite-sparse was sufficient for me to get igraph to install (then ran brew link suite-sparse to quickly re-enable).

For anyone encountering this problem with conda rather than brew, I found that suite-sparse was also the culprit:

conda remove suitesparse
conda install -c r r-igraph
conda install suitesparse

vtraag · 2021-03-05T15:54:15Z

I believe this no longer should be any issue. You should be able to install using remotes::install_github("igraph/rigraph@master"), which at the time of writing contains the development version 1.2.6.9108. It now links explicitly to the internal suitesparse, and we no longer vendor CHOLMOD, so I think this should no longer be a problem. Please do give it a try @pat-s, @ktmeaton, @ivirshup and @rustyconover . If you do run into any issues, feel free to re-open this issue.

bvaldebenitom · 2021-04-09T14:13:25Z

@vtraag I stumbled upon the same issue, and using the "remotes" command results in

Error: (converted from warning) Setting LC_CTYPE failed, using "C"
Execution halted
Error: Failed to install 'igraph' from GitHub:
  (converted from warning) installation of package '/var/folders/b5/718shs9n01jfp6zqss98_y_m0000gn/T//Rtmps3Scpt/file74ff6386968d/igraph_1.2.6.9114.tar.gz' had non-zero exit status

gaborcsardi · 2021-04-09T14:16:44Z

@bvaldebenitom That's not an igraph issue. Update remotes to version 2.3.0 and try again.

bvaldebenitom · 2021-04-09T14:22:09Z

@gaborcsardi thanks for the quick reply.. That worked!!

gaborcsardi closed this as completed Jan 21, 2016

rundel mentioned this issue Mar 1, 2016

include directories listed in CFLAGS and CXXFLAGS instead of PKG_CPPFLAGS #111

Closed

rundel mentioned this issue Mar 4, 2016

Change Makevars.in to use CPPFLAGS #146

Closed

geoHeil mentioned this issue Oct 26, 2016

cant install on osx #173

Closed

pboesu mentioned this issue Sep 17, 2019

R package igraph fails to compile cedadev/ceda-jaspy-envs#31

Closed

GroteGnoom mentioned this issue Jun 8, 2021

Compilation on Mac OS Bug Sur fails #465

Closed

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Fails to install on Mac OS X 10.11 #135

Fails to install on Mac OS X 10.11 #135

rustyconover commented Jan 8, 2016

gaborcsardi commented Jan 21, 2016

rundel commented Feb 27, 2016

rundel commented Mar 1, 2016

ivirshup commented Feb 12, 2019

pat-s commented Nov 30, 2019

ktmeaton commented Jul 11, 2020

vtraag commented Mar 5, 2021

bvaldebenitom commented Apr 9, 2021

gaborcsardi commented Apr 9, 2021

bvaldebenitom commented Apr 9, 2021

Fails to install on Mac OS X 10.11 #135

Fails to install on Mac OS X 10.11 #135

Comments

rustyconover commented Jan 8, 2016

gaborcsardi commented Jan 21, 2016

rundel commented Feb 27, 2016

rundel commented Mar 1, 2016

ivirshup commented Feb 12, 2019

pat-s commented Nov 30, 2019

ktmeaton commented Jul 11, 2020

vtraag commented Mar 5, 2021

bvaldebenitom commented Apr 9, 2021

gaborcsardi commented Apr 9, 2021

bvaldebenitom commented Apr 9, 2021